Starting phenix.real_space_refine on Tue Dec 31 10:48:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qhb_13969/12_2024/7qhb_13969.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qhb_13969/12_2024/7qhb_13969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qhb_13969/12_2024/7qhb_13969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qhb_13969/12_2024/7qhb_13969.map" model { file = "/net/cci-nas-00/data/ceres_data/7qhb_13969/12_2024/7qhb_13969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qhb_13969/12_2024/7qhb_13969.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 94 5.16 5 Cl 4 4.86 5 C 9886 2.51 5 N 2374 2.21 5 O 2694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15052 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2934 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 107 Chain: "B" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2999 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 6, 'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 78 Chain: "I" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1328 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "J" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1328 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 118 Unusual residues: {'79N': 1, 'CYZ': 1, 'OLC': 1, 'PAM': 2} Inner-chain residues flagged as termini: ['pdbres="GLU A1202 "'] Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {'79N': 2, 'CYZ': 1, 'PAM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PAM': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {'PAM': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {'PAM': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: C, D Time building chain proxies: 12.36, per 1000 atoms: 0.82 Number of scatterers: 15052 At special positions: 0 Unit cell: (126.14, 107.06, 134.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 94 16.00 O 2694 8.00 N 2374 7.00 C 9886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.72 Conformation dependent library (CDL) restraints added in 2.1 seconds 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 24 sheets defined 56.9% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 412 through 415 removed outlier: 3.722A pdb=" N ASP A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 478 through 484 removed outlier: 4.040A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 542 Processing helix chain 'A' and resid 568 through 582 removed outlier: 3.639A pdb=" N TRP A 574 " --> pdb=" O PHE A 570 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 621 removed outlier: 3.828A pdb=" N PHE A 603 " --> pdb=" O GLY A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 638 Processing helix chain 'A' and resid 649 through 658 removed outlier: 3.540A pdb=" N GLU A 653 " --> pdb=" O GLY A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 681 through 691 Processing helix chain 'A' and resid 702 through 711 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 789 through 815 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 547 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 624 removed outlier: 4.881A pdb=" N ALA B 621 " --> pdb=" O THR B 617 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE B 623 " --> pdb=" O ASN B 619 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 641 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 677 removed outlier: 3.718A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 697 removed outlier: 3.957A pdb=" N LYS B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 742 through 757 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 819 removed outlier: 3.571A pdb=" N VAL B 792 " --> pdb=" O SER B 788 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 412 through 415 removed outlier: 3.722A pdb=" N ASP C 415 " --> pdb=" O GLU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 457 through 465 Processing helix chain 'C' and resid 478 through 484 removed outlier: 4.040A pdb=" N VAL C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 542 Processing helix chain 'C' and resid 568 through 582 removed outlier: 3.640A pdb=" N TRP C 574 " --> pdb=" O PHE C 570 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 621 removed outlier: 3.828A pdb=" N PHE C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 638 Processing helix chain 'C' and resid 649 through 658 removed outlier: 3.540A pdb=" N GLU C 653 " --> pdb=" O GLY C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 681 through 691 Processing helix chain 'C' and resid 702 through 711 Processing helix chain 'C' and resid 738 through 752 Processing helix chain 'C' and resid 753 through 764 Processing helix chain 'C' and resid 784 through 788 Processing helix chain 'C' and resid 789 through 815 Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 547 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 624 removed outlier: 4.881A pdb=" N ALA D 621 " --> pdb=" O THR D 617 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE D 623 " --> pdb=" O ASN D 619 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 624 " --> pdb=" O LEU D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 641 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 677 removed outlier: 3.717A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 697 removed outlier: 3.957A pdb=" N LYS D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 742 through 757 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 819 removed outlier: 3.571A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 40 removed outlier: 3.698A pdb=" N LEU I 22 " --> pdb=" O GLY I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 128 removed outlier: 3.823A pdb=" N LEU I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 151 Processing helix chain 'I' and resid 155 through 184 removed outlier: 3.828A pdb=" N LEU I 159 " --> pdb=" O ARG I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 234 removed outlier: 3.569A pdb=" N TYR I 206 " --> pdb=" O GLY I 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 40 removed outlier: 3.698A pdb=" N LEU J 22 " --> pdb=" O GLY J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 128 removed outlier: 3.823A pdb=" N LEU J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 151 Processing helix chain 'J' and resid 155 through 184 removed outlier: 3.828A pdb=" N LEU J 159 " --> pdb=" O ARG J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 234 removed outlier: 3.569A pdb=" N TYR J 206 " --> pdb=" O GLY J 202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 440 removed outlier: 6.156A pdb=" N TYR A 391 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLU A 439 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL A 393 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA4, first strand: chain 'A' and resid 493 through 494 Processing sheet with id=AA5, first strand: chain 'A' and resid 698 through 700 removed outlier: 3.794A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 439 through 444 Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.905A pdb=" N ALA B 452 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB1, first strand: chain 'B' and resid 702 through 705 removed outlier: 3.798A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 702 through 705 removed outlier: 3.985A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 436 through 440 removed outlier: 6.156A pdb=" N TYR C 391 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLU C 439 " --> pdb=" O TYR C 391 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL C 393 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB5, first strand: chain 'C' and resid 485 through 487 Processing sheet with id=AB6, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AB7, first strand: chain 'C' and resid 698 through 700 removed outlier: 3.794A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 439 through 444 Processing sheet with id=AB9, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC1, first strand: chain 'D' and resid 452 through 453 removed outlier: 3.905A pdb=" N ALA D 452 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC3, first strand: chain 'D' and resid 702 through 705 removed outlier: 3.798A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 702 through 705 removed outlier: 3.985A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 45 through 49 removed outlier: 3.867A pdb=" N HIS I 83 " --> pdb=" O CYS I 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 45 through 49 removed outlier: 3.868A pdb=" N HIS J 83 " --> pdb=" O CYS J 90 " (cutoff:3.500A) 886 hydrogen bonds defined for protein. 2550 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.58 Time building geometry restraints manager: 5.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2348 1.31 - 1.44: 4367 1.44 - 1.57: 8485 1.57 - 1.71: 8 1.71 - 1.84: 146 Bond restraints: 15354 Sorted by residual: bond pdb=" CB THR C 605 " pdb=" CG2 THR C 605 " ideal model delta sigma weight residual 1.521 1.385 0.136 3.30e-02 9.18e+02 1.70e+01 bond pdb=" CG LEU B 789 " pdb=" CD1 LEU B 789 " ideal model delta sigma weight residual 1.521 1.385 0.136 3.30e-02 9.18e+02 1.69e+01 bond pdb=" CG LEU D 789 " pdb=" CD1 LEU D 789 " ideal model delta sigma weight residual 1.521 1.385 0.136 3.30e-02 9.18e+02 1.69e+01 bond pdb=" CB THR A 605 " pdb=" CG2 THR A 605 " ideal model delta sigma weight residual 1.521 1.386 0.135 3.30e-02 9.18e+02 1.68e+01 bond pdb=" CB THR B 609 " pdb=" CG2 THR B 609 " ideal model delta sigma weight residual 1.521 1.386 0.135 3.30e-02 9.18e+02 1.68e+01 ... (remaining 15349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 20101 2.71 - 5.43: 567 5.43 - 8.14: 92 8.14 - 10.85: 10 10.85 - 13.57: 2 Bond angle restraints: 20772 Sorted by residual: angle pdb=" C10 79N B 904 " pdb=" C9 79N B 904 " pdb=" C8 79N B 904 " ideal model delta sigma weight residual 128.02 141.59 -13.57 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C10 79N A1206 " pdb=" C9 79N A1206 " pdb=" C8 79N A1206 " ideal model delta sigma weight residual 128.02 141.59 -13.57 3.00e+00 1.11e-01 2.05e+01 angle pdb=" N SER D 741 " pdb=" CA SER D 741 " pdb=" C SER D 741 " ideal model delta sigma weight residual 113.02 108.75 4.27 1.20e+00 6.94e-01 1.27e+01 angle pdb=" N SER B 741 " pdb=" CA SER B 741 " pdb=" C SER B 741 " ideal model delta sigma weight residual 113.02 108.75 4.27 1.20e+00 6.94e-01 1.27e+01 angle pdb=" CG ARG J 122 " pdb=" CD ARG J 122 " pdb=" NE ARG J 122 " ideal model delta sigma weight residual 112.00 119.81 -7.81 2.20e+00 2.07e-01 1.26e+01 ... (remaining 20767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.73: 8454 24.73 - 49.45: 463 49.45 - 74.18: 73 74.18 - 98.90: 18 98.90 - 123.63: 20 Dihedral angle restraints: 9028 sinusoidal: 3414 harmonic: 5614 Sorted by residual: dihedral pdb=" C THR B 744 " pdb=" N THR B 744 " pdb=" CA THR B 744 " pdb=" CB THR B 744 " ideal model delta harmonic sigma weight residual -122.00 -133.36 11.36 0 2.50e+00 1.60e-01 2.07e+01 dihedral pdb=" C THR D 744 " pdb=" N THR D 744 " pdb=" CA THR D 744 " pdb=" CB THR D 744 " ideal model delta harmonic sigma weight residual -122.00 -133.30 11.30 0 2.50e+00 1.60e-01 2.04e+01 dihedral pdb=" N2 CYZ A1203 " pdb=" C8 CYZ A1203 " pdb=" N1 CYZ A1203 " pdb=" S1 CYZ A1203 " ideal model delta sinusoidal sigma weight residual 55.73 -67.90 123.63 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 9025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1989 0.084 - 0.168: 332 0.168 - 0.252: 65 0.252 - 0.336: 4 0.336 - 0.420: 4 Chirality restraints: 2394 Sorted by residual: chirality pdb=" C1 CYZ B 902 " pdb=" C2 CYZ B 902 " pdb=" C6 CYZ B 902 " pdb=" C8 CYZ B 902 " both_signs ideal model delta sigma weight residual False 2.79 2.37 0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" C1 CYZ D 902 " pdb=" C2 CYZ D 902 " pdb=" C6 CYZ D 902 " pdb=" C8 CYZ D 902 " both_signs ideal model delta sigma weight residual False 2.79 2.38 0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" CB THR C 605 " pdb=" CA THR C 605 " pdb=" OG1 THR C 605 " pdb=" CG2 THR C 605 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 2391 not shown) Planarity restraints: 2544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP J 111 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.09e+00 pdb=" CG ASP J 111 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP J 111 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP J 111 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP I 111 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" CG ASP I 111 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP I 111 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP I 111 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 403 " -0.039 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO D 404 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO D 404 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 404 " -0.029 5.00e-02 4.00e+02 ... (remaining 2541 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 178 2.60 - 3.18: 14756 3.18 - 3.75: 23237 3.75 - 4.33: 32386 4.33 - 4.90: 54353 Nonbonded interactions: 124910 Sorted by model distance: nonbonded pdb=" SG CYS J 52 " pdb=" SG CYS J 91 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS I 52 " pdb=" SG CYS I 91 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS D 718 " pdb=" SG CYS D 773 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS C 714 " pdb=" SG CYS C 769 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS I 90 " pdb=" SG CYS I 100 " model vdw 2.035 3.760 ... (remaining 124905 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 390 or resid 393 through 398 or resid 400 through 403 or r \ esid 405 through 407 or (resid 412 and (name N or name CA or name C or name O or \ name CB )) or resid 413 through 414 or resid 416 through 422 or resid 424 throu \ gh 431 or resid 433 or resid 436 or resid 438 or resid 440 through 441 or resid \ 443 through 450 or resid 452 through 454 or resid 456 through 466 or resid 468 t \ hrough 469 or resid 471 or resid 473 through 522 or (resid 523 and (name N or na \ me CA or name C or name O or name CB )) or resid 524 through 542 or (resid 566 a \ nd (name N or name CA or name C or name O or name CB )) or resid 567 through 581 \ or resid 583 through 635 or resid 637 through 646 or resid 649 through 652 or ( \ resid 653 and (name N or name CA or name C or name O or name CB )) or resid 654 \ through 656 or (resid 657 and (name N or name CA or name C or name O or name CB \ )) or resid 658 through 663 or resid 665 through 670 or resid 672 through 682 or \ resid 684 through 685 or resid 688 through 709 or (resid 710 through 712 and (n \ ame N or name CA or name C or name O or name CB )) or resid 713 through 714 or ( \ resid 715 and (name N or name CA or name C or name O or name CB )) or resid 716 \ through 736 or resid 738 or resid 741 through 747 or (resid 748 and (name N or n \ ame CA or name C or name O or name CB )) or resid 749 through 753 or (resid 754 \ and (name N or name CA or name C or name O or name CB )) or resid 755 through 75 \ 9 or resid 761 through 764 or (resid 765 through 766 and (name N or name CA or n \ ame C or name O or name CB )) or resid 767 through 769 or resid 779 through 783 \ or (resid 784 and (name N or name CA or name C or name O or name CB )) or resid \ 785 through 795 or resid 797 through 811 or (resid 812 and (name N or name CA or \ name C or name O or name CB )) or resid 813 through 814 or (resid 815 and (name \ N or name CA or name C or name O or name CB )) or resid 1202 through 1203)) selection = (chain 'B' and (resid 394 or resid 397 through 402 or resid 404 through 407 or r \ esid 409 through 411 or resid 416 through 418 or resid 420 through 426 or resid \ 428 through 430 or (resid 431 and (name N or name CA or name C or name O or name \ CB )) or resid 432 through 435 or resid 437 or resid 440 or resid 442 or resid \ 444 through 445 or resid 447 through 448 or (resid 449 and (name N or name CA or \ name C or name O or name CB )) or resid 450 through 453 or (resid 454 and (name \ N or name CA or name C or name O or name CB )) or resid 456 through 457 or (res \ id 458 and (name N or name CA or name C or name O or name CB )) or resid 460 thr \ ough 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) \ or resid 467 through 470 or resid 472 through 473 or resid 475 or resid 477 thro \ ugh 504 or (resid 505 through 506 and (name N or name CA or name C or name O or \ name CB )) or resid 507 or (resid 508 through 509 and (name N or name CA or name \ C or name O or name CB )) or resid 510 through 546 or resid 570 through 585 or \ resid 587 through 593 or (resid 594 and (name N or name CA or name C or name O o \ r name CB )) or resid 595 through 632 or (resid 633 through 634 and (name N or n \ ame CA or name C or name O or name CB )) or resid 635 through 636 or (resid 637 \ through 639 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 1 through 643 or (resid 644 and (name N or name CA or name C or name O or name C \ B )) or resid 645 through 650 or resid 653 through 655 or (resid 656 through 657 \ and (name N or name CA or name C or name O or name CB )) or resid 658 through 6 \ 67 or (resid 669 through 670 and (name N or name CA or name C or name O or name \ CB )) or resid 671 through 673 or (resid 674 and (name N or name CA or name C or \ name O or name CB )) or resid 676 through 686 or (resid 688 and (name N or name \ CA or name C or name O or name CB )) or resid 689 or resid 692 through 693 or ( \ resid 694 through 697 and (name N or name CA or name C or name O or name CB )) o \ r resid 698 or (resid 699 and (name N or name CA or name C or name O or name CB \ )) or resid 700 through 709 or (resid 710 and (name N or name CA or name C or na \ me O or name CB )) or resid 711 through 737 or (resid 738 and (name N or name CA \ or name C or name O or name CB )) or resid 739 through 740 or resid 742 or resi \ d 745 through 760 or (resid 761 and (name N or name CA or name C or name O or na \ me CB )) or resid 762 through 763 or resid 765 through 799 or resid 801 through \ 812 or (resid 813 and (name N or name CA or name C or name O or name CB )) or re \ sid 814 through 817 or (resid 818 through 819 and (name N or name CA or name C o \ r name O or name CB )) or resid 901 or resid 902)) selection = (chain 'C' and (resid 390 or resid 393 through 398 or resid 400 through 403 or r \ esid 405 through 407 or (resid 412 and (name N or name CA or name C or name O or \ name CB )) or resid 413 through 414 or resid 416 through 422 or resid 424 throu \ gh 431 or resid 433 or resid 436 or resid 438 or resid 440 through 441 or resid \ 443 through 450 or resid 452 through 454 or resid 456 through 466 or resid 468 t \ hrough 469 or resid 471 or resid 473 through 522 or (resid 523 and (name N or na \ me CA or name C or name O or name CB )) or resid 524 through 542 or (resid 566 a \ nd (name N or name CA or name C or name O or name CB )) or resid 567 through 581 \ or resid 583 through 635 or resid 637 through 646 or resid 649 through 652 or ( \ resid 653 and (name N or name CA or name C or name O or name CB )) or resid 654 \ through 656 or (resid 657 and (name N or name CA or name C or name O or name CB \ )) or resid 658 through 663 or resid 665 through 670 or resid 672 through 682 or \ resid 684 through 685 or resid 688 through 709 or (resid 710 through 712 and (n \ ame N or name CA or name C or name O or name CB )) or resid 713 through 714 or ( \ resid 715 and (name N or name CA or name C or name O or name CB )) or resid 716 \ through 736 or resid 738 or resid 741 through 747 or (resid 748 and (name N or n \ ame CA or name C or name O or name CB )) or resid 749 through 753 or (resid 754 \ and (name N or name CA or name C or name O or name CB )) or resid 755 through 75 \ 9 or resid 761 through 764 or (resid 765 through 766 and (name N or name CA or n \ ame C or name O or name CB )) or resid 767 through 769 or resid 779 through 783 \ or (resid 784 and (name N or name CA or name C or name O or name CB )) or resid \ 785 through 795 or resid 797 through 811 or (resid 812 and (name N or name CA or \ name C or name O or name CB )) or resid 813 through 814 or (resid 815 and (name \ N or name CA or name C or name O or name CB )) or resid 1202 through 1203)) selection = (chain 'D' and (resid 394 or resid 397 through 402 or resid 404 through 407 or r \ esid 409 through 411 or resid 416 through 418 or resid 420 through 426 or resid \ 428 through 430 or (resid 431 and (name N or name CA or name C or name O or name \ CB )) or resid 432 through 435 or resid 437 or resid 440 or resid 442 or resid \ 444 through 445 or resid 447 through 448 or (resid 449 and (name N or name CA or \ name C or name O or name CB )) or resid 450 through 453 or (resid 454 and (name \ N or name CA or name C or name O or name CB )) or resid 456 through 457 or (res \ id 458 and (name N or name CA or name C or name O or name CB )) or resid 460 thr \ ough 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) \ or resid 467 through 470 or resid 472 through 473 or resid 475 or resid 477 thro \ ugh 504 or (resid 505 through 506 and (name N or name CA or name C or name O or \ name CB )) or resid 507 or (resid 508 through 509 and (name N or name CA or name \ C or name O or name CB )) or resid 510 through 546 or resid 570 through 585 or \ resid 587 through 593 or (resid 594 and (name N or name CA or name C or name O o \ r name CB )) or resid 595 through 632 or (resid 633 through 634 and (name N or n \ ame CA or name C or name O or name CB )) or resid 635 through 636 or (resid 637 \ through 639 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 1 through 643 or (resid 644 and (name N or name CA or name C or name O or name C \ B )) or resid 645 through 650 or resid 653 through 655 or (resid 656 through 657 \ and (name N or name CA or name C or name O or name CB )) or resid 658 through 6 \ 67 or (resid 669 through 670 and (name N or name CA or name C or name O or name \ CB )) or resid 671 through 673 or (resid 674 and (name N or name CA or name C or \ name O or name CB )) or resid 676 through 686 or (resid 688 and (name N or name \ CA or name C or name O or name CB )) or resid 689 or resid 692 through 693 or ( \ resid 694 through 697 and (name N or name CA or name C or name O or name CB )) o \ r resid 698 or (resid 699 and (name N or name CA or name C or name O or name CB \ )) or resid 700 through 709 or (resid 710 and (name N or name CA or name C or na \ me O or name CB )) or resid 711 through 737 or (resid 738 and (name N or name CA \ or name C or name O or name CB )) or resid 739 through 740 or resid 742 or resi \ d 745 through 760 or (resid 761 and (name N or name CA or name C or name O or na \ me CB )) or resid 762 through 763 or resid 765 through 799 or resid 801 through \ 812 or (resid 813 and (name N or name CA or name C or name O or name CB )) or re \ sid 814 through 817 or (resid 818 through 819 and (name N or name CA or name C o \ r name O or name CB )) or resid 901 or resid 902)) } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 40.570 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.146 15354 Z= 1.152 Angle : 1.050 13.568 20772 Z= 0.535 Chirality : 0.068 0.420 2394 Planarity : 0.005 0.058 2544 Dihedral : 17.095 123.629 5438 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.55 % Allowed : 0.69 % Favored : 98.76 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.18), residues: 1926 helix: -0.28 (0.15), residues: 1056 sheet: -2.63 (0.35), residues: 172 loop : -2.55 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 605 HIS 0.007 0.002 HIS J 83 PHE 0.023 0.003 PHE D 541 TYR 0.039 0.003 TYR B 700 ARG 0.027 0.001 ARG J 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 284 time to evaluate : 1.695 Fit side-chains REVERT: B 591 ILE cc_start: 0.7825 (tp) cc_final: 0.7591 (tp) REVERT: B 642 GLN cc_start: 0.7292 (pp30) cc_final: 0.6871 (pp30) REVERT: B 766 TRP cc_start: 0.6293 (m100) cc_final: 0.6048 (m100) REVERT: D 591 ILE cc_start: 0.7818 (tp) cc_final: 0.7575 (tp) REVERT: D 642 GLN cc_start: 0.7290 (pp30) cc_final: 0.6869 (pp30) REVERT: D 766 TRP cc_start: 0.6330 (m100) cc_final: 0.6035 (m100) outliers start: 8 outliers final: 2 residues processed: 286 average time/residue: 0.2813 time to fit residues: 120.5312 Evaluate side-chains 243 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 241 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain D residue 744 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 20 GLN I 105 HIS I 172 ASN ** I 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN J 105 HIS ** J 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15354 Z= 0.241 Angle : 0.606 9.626 20772 Z= 0.311 Chirality : 0.044 0.200 2394 Planarity : 0.005 0.044 2544 Dihedral : 13.601 102.813 2518 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.10 % Allowed : 9.94 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.20), residues: 1926 helix: 1.64 (0.16), residues: 1068 sheet: -2.56 (0.35), residues: 156 loop : -1.59 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 605 HIS 0.013 0.002 HIS I 83 PHE 0.011 0.001 PHE A 542 TYR 0.016 0.001 TYR C 401 ARG 0.005 0.000 ARG J 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 278 time to evaluate : 1.666 Fit side-chains REVERT: A 496 ILE cc_start: 0.8326 (mm) cc_final: 0.7949 (pt) REVERT: A 711 ARG cc_start: 0.3383 (mmp-170) cc_final: 0.3023 (mmp80) REVERT: A 812 TYR cc_start: 0.6387 (t80) cc_final: 0.6137 (t80) REVERT: A 813 LYS cc_start: 0.6065 (mtpp) cc_final: 0.5212 (tttt) REVERT: B 642 GLN cc_start: 0.7425 (pp30) cc_final: 0.6974 (pp30) REVERT: B 674 MET cc_start: 0.7341 (ptm) cc_final: 0.7079 (ptm) REVERT: B 766 TRP cc_start: 0.5897 (m100) cc_final: 0.5531 (m100) REVERT: C 496 ILE cc_start: 0.8333 (mm) cc_final: 0.7956 (pt) REVERT: C 711 ARG cc_start: 0.3284 (mmp-170) cc_final: 0.3025 (mmp80) REVERT: C 812 TYR cc_start: 0.6378 (t80) cc_final: 0.6099 (t80) REVERT: C 813 LYS cc_start: 0.6019 (mtpp) cc_final: 0.5166 (tttt) REVERT: D 642 GLN cc_start: 0.7433 (pp30) cc_final: 0.6976 (pp30) REVERT: D 674 MET cc_start: 0.7355 (ptm) cc_final: 0.7129 (ptm) REVERT: D 766 TRP cc_start: 0.5899 (m100) cc_final: 0.5531 (m100) REVERT: I 42 ASP cc_start: 0.7249 (p0) cc_final: 0.6281 (p0) REVERT: J 42 ASP cc_start: 0.7180 (p0) cc_final: 0.6203 (p0) outliers start: 16 outliers final: 6 residues processed: 282 average time/residue: 0.2822 time to fit residues: 117.4956 Evaluate side-chains 246 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 240 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 759 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 174 optimal weight: 0.0770 chunk 188 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 105 HIS I 197 ASN J 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15354 Z= 0.327 Angle : 0.598 8.216 20772 Z= 0.307 Chirality : 0.043 0.157 2394 Planarity : 0.004 0.043 2544 Dihedral : 12.778 93.510 2518 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.80 % Allowed : 11.81 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.20), residues: 1926 helix: 1.83 (0.16), residues: 1070 sheet: -2.61 (0.33), residues: 174 loop : -1.31 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 460 HIS 0.010 0.002 HIS I 83 PHE 0.014 0.002 PHE I 29 TYR 0.022 0.002 TYR C 401 ARG 0.004 0.000 ARG I 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 285 time to evaluate : 1.656 Fit side-chains REVERT: A 469 ASP cc_start: 0.5210 (m-30) cc_final: 0.4109 (m-30) REVERT: B 674 MET cc_start: 0.7562 (ptm) cc_final: 0.7361 (ptm) REVERT: B 708 MET cc_start: 0.7346 (mtt) cc_final: 0.7127 (mtt) REVERT: C 469 ASP cc_start: 0.5485 (m-30) cc_final: 0.4416 (m-30) REVERT: I 227 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7637 (mp) REVERT: J 227 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7543 (mp) outliers start: 26 outliers final: 14 residues processed: 297 average time/residue: 0.2693 time to fit residues: 120.6300 Evaluate side-chains 279 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 263 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 784 THR Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain J residue 227 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 83 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 166 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN D 756 GLN ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 HIS ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15354 Z= 0.207 Angle : 0.551 10.519 20772 Z= 0.281 Chirality : 0.041 0.151 2394 Planarity : 0.004 0.042 2544 Dihedral : 12.049 86.584 2518 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.62 % Allowed : 12.71 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.20), residues: 1926 helix: 2.10 (0.16), residues: 1074 sheet: -2.35 (0.35), residues: 156 loop : -1.07 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 762 HIS 0.011 0.002 HIS J 83 PHE 0.011 0.001 PHE B 515 TYR 0.031 0.001 TYR C 707 ARG 0.009 0.000 ARG A 739 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 266 time to evaluate : 1.651 Fit side-chains REVERT: A 469 ASP cc_start: 0.5591 (m-30) cc_final: 0.4517 (m-30) REVERT: A 492 MET cc_start: 0.7882 (ttm) cc_final: 0.7673 (ttm) REVERT: A 813 LYS cc_start: 0.5822 (mtpp) cc_final: 0.4884 (tttt) REVERT: B 483 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8121 (tt) REVERT: B 708 MET cc_start: 0.7255 (mtt) cc_final: 0.6996 (mtt) REVERT: C 469 ASP cc_start: 0.5587 (m-30) cc_final: 0.4502 (m-30) REVERT: C 813 LYS cc_start: 0.5784 (mtpp) cc_final: 0.4890 (tttt) REVERT: D 483 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8107 (tt) REVERT: I 35 MET cc_start: 0.7454 (tpt) cc_final: 0.7247 (tpt) REVERT: I 42 ASP cc_start: 0.6786 (p0) cc_final: 0.6576 (p0) REVERT: I 48 ARG cc_start: 0.7285 (ttm110) cc_final: 0.7013 (ttm-80) REVERT: I 227 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7585 (mp) REVERT: J 227 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7638 (mp) outliers start: 38 outliers final: 20 residues processed: 285 average time/residue: 0.2749 time to fit residues: 117.4545 Evaluate side-chains 279 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 255 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 227 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 0.4980 chunk 105 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN B 756 GLN C 571 ASN D 756 GLN ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15354 Z= 0.272 Angle : 0.575 9.258 20772 Z= 0.290 Chirality : 0.042 0.211 2394 Planarity : 0.004 0.039 2544 Dihedral : 11.608 72.536 2518 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.62 % Allowed : 13.74 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.20), residues: 1926 helix: 1.99 (0.16), residues: 1072 sheet: -2.33 (0.39), residues: 140 loop : -0.97 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 762 HIS 0.009 0.001 HIS I 83 PHE 0.016 0.001 PHE B 515 TYR 0.035 0.002 TYR C 707 ARG 0.007 0.000 ARG J 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 1.620 Fit side-chains REVERT: A 469 ASP cc_start: 0.5659 (m-30) cc_final: 0.4519 (m-30) REVERT: A 641 ILE cc_start: 0.4812 (mp) cc_final: 0.4610 (mt) REVERT: B 483 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8276 (tt) REVERT: C 469 ASP cc_start: 0.5724 (m-30) cc_final: 0.4556 (m-30) REVERT: C 641 ILE cc_start: 0.4780 (mp) cc_final: 0.4560 (mt) REVERT: D 483 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8279 (tt) REVERT: I 35 MET cc_start: 0.7659 (tpt) cc_final: 0.7423 (tpt) REVERT: I 42 ASP cc_start: 0.6856 (p0) cc_final: 0.6621 (p0) REVERT: I 103 ILE cc_start: 0.8139 (mt) cc_final: 0.7912 (mt) REVERT: I 227 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7592 (mp) REVERT: J 227 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7698 (mp) outliers start: 38 outliers final: 25 residues processed: 272 average time/residue: 0.2824 time to fit residues: 114.9762 Evaluate side-chains 272 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 243 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain J residue 227 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.0370 chunk 167 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 154 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 97 optimal weight: 0.4980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN D 756 GLN ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15354 Z= 0.172 Angle : 0.525 9.481 20772 Z= 0.267 Chirality : 0.041 0.196 2394 Planarity : 0.004 0.039 2544 Dihedral : 10.571 58.707 2518 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.83 % Allowed : 13.81 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.20), residues: 1926 helix: 2.22 (0.16), residues: 1076 sheet: -2.15 (0.38), residues: 142 loop : -0.84 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 203 HIS 0.010 0.002 HIS I 83 PHE 0.012 0.001 PHE B 515 TYR 0.037 0.001 TYR A 707 ARG 0.008 0.000 ARG A 711 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 267 time to evaluate : 1.546 Fit side-chains REVERT: A 469 ASP cc_start: 0.5655 (m-30) cc_final: 0.4493 (m-30) REVERT: A 711 ARG cc_start: 0.3317 (mmp-170) cc_final: 0.3111 (mmp-170) REVERT: A 813 LYS cc_start: 0.5768 (mtpp) cc_final: 0.4776 (tttt) REVERT: B 483 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8264 (tt) REVERT: C 469 ASP cc_start: 0.5766 (m-30) cc_final: 0.4602 (m-30) REVERT: C 813 LYS cc_start: 0.5949 (mtpp) cc_final: 0.4994 (tttt) REVERT: D 483 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8267 (tt) REVERT: I 227 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7513 (mp) REVERT: J 48 ARG cc_start: 0.7069 (ttm-80) cc_final: 0.6819 (ttm110) REVERT: J 227 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7621 (mp) outliers start: 41 outliers final: 26 residues processed: 282 average time/residue: 0.2587 time to fit residues: 109.8617 Evaluate side-chains 300 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 270 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain J residue 227 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN D 756 GLN ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15354 Z= 0.304 Angle : 0.571 9.736 20772 Z= 0.291 Chirality : 0.043 0.197 2394 Planarity : 0.004 0.039 2544 Dihedral : 10.742 59.841 2518 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.90 % Allowed : 14.99 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.20), residues: 1926 helix: 2.04 (0.16), residues: 1072 sheet: -2.24 (0.38), residues: 148 loop : -0.95 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 203 HIS 0.008 0.001 HIS I 83 PHE 0.017 0.002 PHE B 515 TYR 0.039 0.002 TYR C 707 ARG 0.006 0.000 ARG J 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 264 time to evaluate : 1.660 Fit side-chains REVERT: A 469 ASP cc_start: 0.5823 (m-30) cc_final: 0.4623 (m-30) REVERT: A 711 ARG cc_start: 0.3585 (mmp-170) cc_final: 0.3013 (mmp-170) REVERT: A 728 TYR cc_start: 0.8459 (m-10) cc_final: 0.8243 (m-10) REVERT: B 483 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8397 (tt) REVERT: C 469 ASP cc_start: 0.5869 (m-30) cc_final: 0.4629 (m-30) REVERT: D 483 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8393 (tt) REVERT: I 227 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7653 (mp) REVERT: J 227 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7651 (mp) outliers start: 42 outliers final: 29 residues processed: 281 average time/residue: 0.2657 time to fit residues: 112.1120 Evaluate side-chains 287 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 254 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 227 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 145 optimal weight: 0.4980 chunk 168 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN D 756 GLN I 105 HIS ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15354 Z= 0.210 Angle : 0.537 9.874 20772 Z= 0.274 Chirality : 0.041 0.166 2394 Planarity : 0.004 0.041 2544 Dihedral : 10.343 59.830 2518 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.83 % Allowed : 15.12 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.20), residues: 1926 helix: 2.16 (0.16), residues: 1074 sheet: -2.19 (0.38), residues: 148 loop : -0.90 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 203 HIS 0.009 0.002 HIS J 83 PHE 0.015 0.001 PHE D 515 TYR 0.046 0.001 TYR A 707 ARG 0.007 0.000 ARG C 739 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 261 time to evaluate : 1.793 Fit side-chains REVERT: A 469 ASP cc_start: 0.5940 (m-30) cc_final: 0.4707 (m-30) REVERT: A 711 ARG cc_start: 0.3574 (mmp-170) cc_final: 0.3358 (mmp-170) REVERT: A 813 LYS cc_start: 0.6056 (mtpp) cc_final: 0.5082 (tttt) REVERT: B 483 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8279 (tt) REVERT: C 469 ASP cc_start: 0.5898 (m-30) cc_final: 0.4679 (m-30) REVERT: D 483 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8280 (tt) REVERT: I 227 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7664 (mp) REVERT: J 227 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7663 (mp) outliers start: 41 outliers final: 29 residues processed: 280 average time/residue: 0.2711 time to fit residues: 113.8530 Evaluate side-chains 283 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 250 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain J residue 227 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 75 optimal weight: 0.0030 chunk 135 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN D 756 GLN ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 HIS ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 198 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15354 Z= 0.246 Angle : 0.548 8.473 20772 Z= 0.280 Chirality : 0.042 0.163 2394 Planarity : 0.004 0.039 2544 Dihedral : 10.278 59.997 2518 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.69 % Allowed : 15.40 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.20), residues: 1926 helix: 2.09 (0.16), residues: 1074 sheet: -2.13 (0.38), residues: 148 loop : -0.93 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 203 HIS 0.012 0.002 HIS I 105 PHE 0.014 0.001 PHE D 515 TYR 0.044 0.002 TYR C 707 ARG 0.007 0.001 ARG C 739 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 261 time to evaluate : 1.653 Fit side-chains REVERT: A 469 ASP cc_start: 0.5934 (m-30) cc_final: 0.4664 (m-30) REVERT: B 483 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8219 (tt) REVERT: C 469 ASP cc_start: 0.5872 (m-30) cc_final: 0.4569 (m-30) REVERT: C 492 MET cc_start: 0.7828 (ttm) cc_final: 0.7603 (ttm) REVERT: D 483 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8225 (tt) REVERT: I 48 ARG cc_start: 0.7092 (ttm-80) cc_final: 0.6644 (ttm-80) REVERT: I 227 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7679 (mp) REVERT: J 227 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7699 (mp) outliers start: 39 outliers final: 31 residues processed: 280 average time/residue: 0.2691 time to fit residues: 113.0888 Evaluate side-chains 287 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 252 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain J residue 227 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 126 optimal weight: 0.9990 chunk 191 optimal weight: 0.5980 chunk 176 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 93 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 ASN B 756 GLN D 756 GLN ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 HIS I 198 HIS ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15354 Z= 0.270 Angle : 0.563 10.284 20772 Z= 0.289 Chirality : 0.042 0.163 2394 Planarity : 0.004 0.040 2544 Dihedral : 10.132 59.108 2518 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.69 % Allowed : 15.75 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.20), residues: 1926 helix: 2.04 (0.16), residues: 1074 sheet: -2.06 (0.37), residues: 164 loop : -0.88 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 203 HIS 0.012 0.002 HIS I 105 PHE 0.013 0.001 PHE D 515 TYR 0.045 0.002 TYR A 707 ARG 0.007 0.001 ARG I 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 263 time to evaluate : 1.658 Fit side-chains REVERT: A 469 ASP cc_start: 0.5892 (m-30) cc_final: 0.5206 (m-30) REVERT: A 813 LYS cc_start: 0.6082 (mtpp) cc_final: 0.5160 (tttt) REVERT: B 483 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8084 (tt) REVERT: C 469 ASP cc_start: 0.5878 (m-30) cc_final: 0.5198 (m-30) REVERT: C 492 MET cc_start: 0.7841 (ttm) cc_final: 0.7609 (ttm) REVERT: C 813 LYS cc_start: 0.6084 (mtpp) cc_final: 0.5160 (tttt) REVERT: D 483 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8052 (tt) REVERT: I 227 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7642 (mp) REVERT: J 227 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7749 (mp) outliers start: 39 outliers final: 34 residues processed: 280 average time/residue: 0.2618 time to fit residues: 109.2542 Evaluate side-chains 290 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 252 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 198 HIS Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain J residue 227 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 156 optimal weight: 0.3980 chunk 19 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN D 756 GLN ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 198 HIS ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.208634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.179944 restraints weight = 18219.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.179914 restraints weight = 37356.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.181047 restraints weight = 28554.463| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15354 Z= 0.228 Angle : 0.544 8.512 20772 Z= 0.281 Chirality : 0.042 0.168 2394 Planarity : 0.004 0.070 2544 Dihedral : 9.909 59.347 2518 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.56 % Allowed : 16.16 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.20), residues: 1926 helix: 2.09 (0.16), residues: 1074 sheet: -1.99 (0.38), residues: 164 loop : -0.88 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 203 HIS 0.009 0.001 HIS J 83 PHE 0.016 0.001 PHE D 491 TYR 0.049 0.002 TYR C 707 ARG 0.009 0.000 ARG A 711 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2984.13 seconds wall clock time: 56 minutes 15.22 seconds (3375.22 seconds total)